You have several assumptions in your question.
First: "deadly virus that can never be reversed, cured, or stopped". It's a basic assumption in your question, but it is not supported. There is no such thing. Just from a biological basis a virus depends on its host to survive, if it kills the host the virus dies too. This balance prevents any virus from getting out of control.
Second: "Quantum physics tells us all possible outcomes do occur in alternate timelines." This isn't true either. First, quantum physics tells us no such thing, it's a theory, but it has not even a shred of evidence except for "you can use this theory to solve a paradox (specifically single photon scattering)".
Third: "all possible outcomes". Even if the theory is true, all possible outcomes do not occur. Only things that are random at a quantum level are duplicated in this way. But the vast majority of actions are not dependent on quantum randomness and are identical in all universes.
There is a theory (and I VERY strongly emphasize the word theory here, this is a very controversial idea) that free will is basically quantum randomness. Without randomness you would assume that everything is predetermined since all physical interactions are deterministic. Why should a human brain be any different? So what is free will? It's quantum randomness, which is not deterministic. (The alternative non-religious explanation for free will is that there is no such thing.)
Except that free will is actually a function of the soul, and the soul is not subject to quantum randomness, so any action a person takes in one world is likely to be the same in all of them. Including the actions of Mr. John.
Fourth: "our spirits get transported" Transported to what? Wouldn't that world already have people in it? And if not, it's completely equivalent to simply stopping John in this world. (How would you tell the difference?)
Fifth: "Hashem doesn't want to break one of his fundamental laws" Can't Hashem give a human the power to stop John? Hashem has the ability to do anything, including giving a human the ability to stop an unstopable virus. (The virus was created by man after all - since when does man have the ability to create something absolute?)